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Europejskie Centrum Bioinformatyki i Genomiki

Instytut Informatyki Politechniki Poznańskiej

Wielkopolskie Centrum Zaawansowanych Technologii

Institute of Bioorganic Chemistry,
Polish Academy of Sciences
Z. Noskowskiego 12/14
61-704 Poznań
tel centrala: (+48) 61 852 85 03
fax: (+48) 61 852 05 32
e-mail: ibch@ibch.poznan.pl

Sekretariat Dyrektora, tel: 61 852 89 19

Department of Functional Transcriptomics

Dr. habil. Kamilla Bąkowska-Żywicka

Head of Department
bakowska@ibch.poznan.pl
Phone: 61 8291866

Anna Wasilewska MSc

PhD student

Piotr Pietras MSc, BEng.
PhD student

Klementyna Marciniak MSc, BEng.

biologist/ PhD student

Dr. Anna Mleczko
biologist

mgr inż. Kamila Pepłowska
biologist

mgr inż. Julian Zacharjasz
biologist

Dr. Piotr Machtel
asystent

• Mleczko AM, Machtel P, Walkowiak M, Wasilewska A, Pietras PJ, Bąkowska-Żywicka K. Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression. Sci Rep. 2019 Dec 5;9(1):18397. doi: 10.1038/s41598-019-54924-2.

• Mleczko AM, Celichowski P, Bąkowska-Żywicka K. Transfer RNA-derived fragments target regulate ribosome-associated aminoacyl-transfer RNA synthetases. Biochim Biophys Acta Gene Regul Mech. 2018 Jun 6. pii: S1874-9399(17)30380-2. doi: 10.1016/j.bbagrm.2018.06.001

• Bąkowska-Żywicka K, Mleczko AM, Kasprzyk M, Machtel P, Żywicki M, Twardowski T. The widespread occurrence of tRNA-derived fragments in Saccharomyces cerevisiae. FEBS Open Bio. 2016 Oct 21;6(12):1186-1200. doi: 10.1002/2211-5463.12127

• Mleczko AM, Bąkowska-Żywicka K. When small RNAs become smaller: emerging functions of snoRNAs and their derivatives. Acta Biochim Pol. 2016;63(4):601-607.

• Bąkowska-Żywicka K, Kasprzyk M, Twardowski T. tRNA-derived short RNAs bind to Saccharomyces cerevisiae ribosomes in a stress-dependent manner and inhibit protein synthesis in vitro. FEMS Yeast Res. 2016 Sep;16(6). pii: fow077

• Machtel P, Bąkowska-Żywicka K, Żywicki M. Emerging applications of riboswitches – from antibacterial targets to molecular tools. J Appl Genet. 2016 Nov;57(4):531-541

• Mleczko AM, Celichowski P, Bąkowska-Żywicka K. Ex-translational function of tRNAs and their fragments in cancer. Acta Biochim Pol. 2014;61(2):211-6.

• Pircher A, Bakowska-Zywicka K, Schneider L, Zywicki M, Polacek N. An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol Cell. 2014 Apr 10;54(1):147-155. doi: 10.1016/j.molcel.2014.02.024

• Zywicki M, Bakowska-Zywicka K, Polacek N. Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res. 2012 May;40(9):4013-24. doi: 10.1093/nar/gks020

• Changes in the ribosomal protein composition and in the ribosome-associated small noncoding RNAs in Saccharomyces cerevisiae as a response to environmental stress NCN – Opus 14
• Designing a new method for direct identification and absolute quantification of premature transcription termination events, following the example of bacterial riboswitches NCN – Preludium 12
• RNA regulatory networks as novel antimicrobial targets in multidrugs resistant bacteria (cooperation with Department of Computational Biology, Biology Faculty  UAM in Poznań). NCN – Opus 13

• regulatory RNAs,
• noncoding RNAs,
• ribosome-associated noncoding RNAs (rancRNA),
• riboswitches

The research profile of the Functional Transcriptomics Team includes the identification and characterization of molecular mechanisms of RNA-based gene expression regulation in model pro- and eukaryotic organisms, as a response to environmental changes. 

Our research interest includes the following topics:

• identification, characterization and determination of the regulatory potential of small ribosome-associated noncoding RNAs (rancRNA) in Saccharomyces cerevisiae under various environmental conditions, with particular emphasis on heterogeneity of ribosomes,

• identification of riboswitches which regulate transcription and translation in model bacterium Bacillus subtilis,

• comprehensive characterization of changes in the transcriptional, translational and regulatory activity induced in response to antibiotic stress and culture in infectious conditions in the drug-resistant strain Staphylococcus aureus, with special emphasis on the therapeutic potential of regulatory RNAs.